Niraj Rai

Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat- and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase nonpersistence. Concurrently, we identify significant associations of urbanization markers with increased abundance of disease-linked taxa, especially Megamonas-correlated with increased blood glucose and lower gut microbiome diversity-which is enriched in SAMBAR over comparative global regions. Overall, microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography, and underscoring the need for community-specific investigations of health impacts.

Background: The Buthidae, is the largest and most widely distributed scorpion family that encompasses more than 1300 species worldwide and includes several medically important scorpions. Though they pose significant public health risks, there is a critical knowledge gap about the species-environmental interactions of Buthidae species in India. The present study addresses this by systematically mapping Buthidae species distributions across Central India in ArcGIS environment and finding out their suitable habitats using Maximum entropy modeling approach. The study also aims to identify the key environmental predictors of habitat suitability using Jackknife analysis. Results: The spatial patterns revealed scattered or an evenly distribution of most of the species except Hottentotta rugiscutis and Buthoscorpio politus , which show more or less a clustered distribution. Species distribution model demonstrated significant variation in minimum ( ≤ 22%) and maximum predictive performances (≥ 83%) across scorpion species. Suitable habitat for all species found to be diffused except H. rugiscutis and B. politus , for which the area under curve value was found to be excellent (≥ 90%) and very good (≥ 80%H. jabalpurensis (56.6%) and the lowest for H. rugiscutis (13%). For most species, hydrological factors like precipitation and relative humidity were key determinants of scorpion distribution in the study area. The result demonstrated clear interspecific variation in model performance and environmental drivers that play a critical role in niche partitioning through microhabitat stratification. Most species were found to be habitat specialists that are adapted to human settlements. Central Madhya Pradesh and Northwest Chhattisgarh emerged as high-risk regions for scorpion envenomation risks. Conclusion: This study brought into light the first predictive framework for medically significant Buthidae scorpions in Central India, integrating field surveys with species distribution modeling to provide critical insights to understand interspecific variation in model performance and environmental drivers in spatial segregation. The overall outcome of the study will no doubt help in management of Buthid scorpions in Central India for their conservation and better addressing of human-scorpion interactions in this region.

The trans-Himalayan region of Ladakh occupies a strategic position at the crossroads of South Asia, the Tibetan Plateau, and Central Asia, with archaeological evidence pointing to long-term cultural exchanges across these regions. However, the human genetic history of Ladakh remains largely unexplored. We generated paleogenomic data from seven individuals recovered from two sites in Western Ladakh - the Old Lady Spider Cave and Hanu - of which six are dated to 531-585 CE and one to the 19th century CE. The older individuals share substantial genetic ancestry with Tibetan groups but also harbor major contributions from two additional sources: one corresponding to the currently-oldest observation of the Ancestral North Indian genetic component that characterizes several present-day populations in North India and Pakistan, and another related to ancient Central Asian groups, with admixture events occurring between ∼2,100-2,500 years ago. In contrast, the later individual falls within a previously described ancient northern Himalayan genetic cline based on ∼1,100-1,300-year-old individuals from Himachal Pradesh, with ancestries related to ancient Tibetan and Steppe-related sources. Stable isotope analysis suggests that these individuals were local to Ladakh in late life and practiced an agro-pastoralist subsistence. Our study establishes that Ladakh’s central role in Eurasian economic and socio-cultural networks was shaped by dynamic and sustained gene flow linking high-altitude Himalayan groups with both lowland South Asia and Inner Asia.

Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Although urbanization is consistently associated with increased abundance of disease-linked taxa, microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat– and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase non-persistence. Microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography and underscoring the need for community-specific investigations of health impacts.

Archaeological and paleogenomic evidence from the Tibetan Plateau and high-altitude Central Himalayas suggest biocultural connections with each other and with lowland East, Central, and South Asia. However, genetic histories at the northern frontier of the Indian Himalayas, which is geographically more proximal to Central and lowland South Asia, remain underexplored. We analyzed genome-wide data from 7 ancient (~2300 to 100 years old) and 10 present-day individuals from the northern Indian Himalayas and one ~3370-year-old individual from the Central Himalayas in Nepal. Ancient and present-day individuals from the northern Himalayas predominantly have Tibetan-related genetic ancestry, likely the source of high-altitude adaptive variants in these individuals, with substantial Steppe-related genetic ancestry that is observed in all individuals dating between ~1300 years and present day. In addition, some present-day individuals have lowland South Asian admixture. Our analyses reveal a dynamic interplay between genetic admixture and continuity in the northern Himalayas.

South Asia is rich in cultural and genetic diversity; however, it is hardly represented in the blooming field of archaeogenetics. The Neolithic site of Burzahom is of high cultural value and archaeological importance and is one of the earliest human settlements in the Kashmir Valley with numerous evidence of migration and cultural assimilation. In our current study, we have reconstructed for the first time the complete mitogenomes of Neolithic, megalithic and medieval individuals from the Burzahom archaeological site in Kashmir. Our findings suggest that Neolithic and Megalithic periods were characterized by predominantly local genetic influence on the maternal gene pool, with some evidence of genetic contact with the Iron Age Swat Valley. While medieval populations showed clear signs of genetic contacts with Swat Valley historical and Central Asian Bronze age populations. Interestingly, Bayesian evolutionary analysis suggests an affinity of one of the medieval samples with a medieval sample from Roopkund Lake; the finding will be more conclusive with more sample evidence. In summary, we propose that the genetics of Neolithic, megalithic and medieval Kashmir agree well with the archaeological evidence of cultural contacts with the Swat Valley and Central Asia.

Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions. Graphical Abstract Illustrating initial sample collection and experimental procedure

The Nicobarese are the major tribal groups in the Nicobar district, situated south of the Andaman group of Islands. Linguistic phylogeny suggests that the linguistic ancestors of the Nicobarese settled the Nicobar archipelago in the early Holocene. So far, genetic research on them is low-resolution and restricted to the haploid DNA markers. Therefore, in the present analysis, we have used the high-resolution biparental (1554 published and 5 newly genotyped Nicobarese individuals) and uniparental genetic markers and looked at the genetic association of Nicobarese with the South and Southeast Asian populations. We report a common ancestral component shared among the Austroasiatic of South and Southeast Asia. Our analyses have suggested that the Nicobarese peoples retain this ancestral Austroasiatic predominant component in their genomes in the highest proportion. On the Southeast Asian mainland, the Htin Mal, who speak an Austroasiatic language of the Khmuic branch, represent a population that has preserved their ethnic distinctness from other groups over time and consequently shown the highest drift with the Nicobarese. The analysis based on haplotypes indicated a significant level of genomic segment sharing across linguistic groups, indicating an ancient broader distribution of Austroasiatic populations in Southeast Asia. Based on the temporal analyses of haploid DNA, it is suggested that the forebears of the Nicobarese people may have arrived on the Nicobar Islands in the last 5000 YBP. Therefore, among the modern populations, the Nicobarese peoples and the Htin Mal language community represent good genetic proxies for ancient Austroasiatics.